Welcoming the apex court order setting up the SIT comprising five CBI officers, he told PTI that "protection of human rights is the first priority" of his government.
The state government will provide "necessary assistance to book the culprits" involved in the alleged extra-judicial killings by security forces, he said.
The government was committed to the welfare of the people of the state, he said.
The apex court directed the CBI director to nominate a team of five officers for the SIT within two weeks, who will lodge the necessary FIRs and complete the investigation into the fake encounters by December 31 this year.
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The apex court gave the direction while hearing a PIL seeking an investigation and compensation for the alleged killings.
The writ petition was filed by human rights groups the Human Rights Alert and the Extra Judicial Execution Victim Families Association.
Describing it as a "historic judgement", he said this time the "focus should be on those who gave the orders to kill, in addition to those security personnel who were just following those instructions".
"The Army will have to open up during the CBI investigation even though its personnel are protected by the Armed Forces Special Powers Act (AFSPA), 1958," Loitongbam said.